August 5, 2006
The Turtles use new technology to create new weapons in an effort to escape the future.

Episode 3
Home Invasion
August 12, 2006
A computer virus traps the Turtles inside the Dojo and they must fight for their lives.

Episode 4
Headlock Prime
September 30, 2006
Raph competes in a professional wrestling tournament, which is interrupted by a banned wrestler looking to prove himself.

Episode 5
Playtime's Over
October 7, 2006
Mikey is excited when a video game sequel is released; the Turtles need a guide to navigate the mall.

Episode 6
Bishop to Knight
October 14, 2006
The Turtles find out that Agent Bishop is alive in the year 2105.

Episode 7
Night of Sh'okanabo!
October 21, 2006
Mikey brings Cody and his three friends to a horror film festival, where they meet Sh'okanabo face to face.

Episode 8
Clash of the Turtle Titans
October 28, 2006
Mikey discovers that someone has taken his old superhero persona, Turtle Titan.

Episode 9
Fly Me to the Moon
November 4, 2006
Cody and the Turtles search for a rare alloy on the moon; Inuwashi Gunjin goes there to make sure they do not return alive.

Episode 10
Invasion of the Body Snatcher!
November 11, 2006
Jammerhead uses the Bodyjacker to take over Darius Dun's body to steal O'Neil Tech's secrets.

Episode 11
The Freaks Come Out at Night
November 25, 2006
Sh'Okanabo implants gene seeds in Mikey, beginning his first test of introducing the seeds into the general population.

Episode 12
Bad Blood
December 2, 2006
The Turtles' psychotic clones try to prove that they are bigger, badder and better than the Turtles.

Episode 13
The Journal
December 9, 2006
The Turtles come across April and Casey's old future-history journal.

Episode 14
The Gaminator
December 16, 2006
Viral sets a trap that digitizes and sucks the Turtles into a prototype game system, the Gaminator.

Episode 15
Graduation Day: Class of 2105
March 24, 2007
Splinter announces that the Turtles will graduate to the next ninja rank, except Michelangelo.
Episode 16
Timing Is Everything
March 31, 2007
Sh'Okanabo unleashes a time storm on New York, putting the Turtles in the middle of chaos.
Episode 17
Enter the Jammerhead
April 7, 2007
Jammerhead escapes from prison and confronts the Turtles during a visit from Starlee's alien family.
Episode 18
Milk Run
April 14, 2007
An intergalactic mercenary enlists the Turtles' help in smuggling a ship full of humanitarian aid past Triceraton gangsters.
Episode 19
The Fall of Darius Dunn
April 21, 2007
When Cody uncovers a secret weapons-manufacturing program, he and his uncle have a showdown over who will ultimately control the O'Neilltech empire.
Episode 20
Turtle X-Tinction
April 28, 2007
Darius Dunn controls Turtle X to exact revenge on his nephew and the Turtles.
Episode 21
Race for Glory
September 8, 2007
Triple Threat crashes a cross-country road race and steals all the cars.
Episode 22
Head of State
September 15, 2007
The Turtles must rescue the president before he loses his head to a sinister figure from their past.
Episode 23
DNA Is Thicker Than Water
October 6, 2007
Dark Leo tries to prove himself by destroying the Turtles from within.
Episode 24
The Cosmic Completist
October 13, 2007
The leader of Inawashi Gunjin asks the turtles for help with a malicious alien.
Episode 25
The Day of Awakening
October 20, 2007
When the entire population of Moonbase Bishop goes missing and the Turtles stage an assault on the base, they find a bigger Sh'Okanabo with an army of drones.
Episode 26
Zixxth Sense
October 27, 2007
Torbin Zixx persuades the turtles to help him recover an experimental matter transmitter.